chrisamiller

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C

bam-window

0 0
bam-window code for getting depth in genomic intervals

biscuit

0 0
C tools for analyzing sodium bisulfite converted sequencing data

kallisto

0 0
Near-optimal RNA-Seq quantification

C++

telseq

0 0
A software for calculating telomere length

Common Workflow Language

analysis-workflows

0 0
MGI's Analysis Workflows and Pipelines managed by the BGA group.

cancer-genomics-workflow

0 0
MGI's CWL Cancer Pipelines.

Dockerfile

docker-genomic-analysis

2 6
Basic docker image for ad-hoc genomic analyses

docker-bamsurgeon

0 0
dockerfile for bamsurgeon

docker-bisulfite

0 0
a fat pipeline for running WGBS analysis

docker-finger

0 0
finger command

docker-fp_filter-cwl

0 0

docker-gdc-client

0 0
docker image for running the gdc client

docker-guideseq

0 0
docker image for https://github.com/aryeelab/guideseq

docker-guideseq-cam

0 0
Image for github.com/chrisamiller/guideseq

docker-hmMHC

0 0
docker container for hmMHC - https://github.com/artyomovlab/hmmhc

docker-homer

0 2
fork of the quay.io homer image, moving annotations to my hardcoded link

docker-how_stranded

0 0
docker for https://github.com/betsig/how_are_we_stranded_here

docker-igv

0 0

docker-phlat

0 0
dockerization of phlat hla typing tool

docker-sambamba-cwl

0 0

docker-synapser

0 0
docker image for R synapser package

HTML

cv

0 0
CV webpage

JavaScript

regexbot

0 0
Slackbot for responding to messages that match regexes

Perl

rtm-cli

8 2
A command-line Remember the Milk client written in perl

bioinfoSnippets

2 2
Short snippets of code useful for bioinformatics and genomics

convertEnsemblGTF

0 0
Convert ensembl GTF from [1,2,3] nomenclature to [chr1, chr2, chr3] nomenclature

docker-cle

0 0
Docker containerization for the CLE

fpfilter-tool

0 0

genome

0 0
Core modules used by the GMS

netChopScraper

0 0
Allows programmatic retrieval of peptide cleavage predictions from the NetChop server at http://www.cbs.dtu.dk/services/NetChop/

Python

docker-R-singlecell

1 0
tools for single-cell RNAseq analysis

docker-haloplex_demux

0 0
Docker container for demultiplexing haloplex data, thanks to ED and HA

docker-r-seurat

0 1
tools for single-cell RNAseq analysis, incl seurat

docker-somatic-llr-filter

0 0
Container for the somatic-llr filter

guideseq

0 0
Analysis pipeline for the GUIDE-seq assay. For news, see:

intervene

0 0
Intervene: a tool for intersection and visualization of multiple genomic region and gene sets

OptiType

0 0
Precision HLA typing from next-generation sequencing data

primerDesign

0 0
A tool to design highly specific PCR primers for the validation of genomic alterations including structural variants

pysamstats

0 0
A fast Python and command-line utility for extracting simple statistics against genome positions based on sequence alignments from a SAM or BAM file.

vcf-annotation-tools

0 0
A set of tools to annotate VCF files with expression and readcount data

R

fishplot

104 34
Create timecourse "fish plots" that show changes in the clonal architecture of tumors

readDepth

24 11
R package for inferring copy number from read depth

copyCat

15 7
a parallel R package for detecting copy-number alterations from short sequencing reads

rnaseq_tutorial

1 1
Informatics for RNA-seq: A web resource for analysis on the cloud. Educational tutorials and working pipelines for RNA-seq analysis including an introduction to: cloud computing, critical file formats, reference genomes, gene annotation, expression, differential expression, alternative splicing, data visualization, and interpretation.

AH_BioPharma

0 0
BioPharma projects

CONICS

0 0
CONICS: COpy-Number analysis In single-Cell RNA-Sequencing

docker-bsseq-r

0 1
docker image for doing bsseq analysis in R

docker-copycat

0 1
docker image for the R copyCat package

docker-rnaseq

0 0
A fat docker image for running RnaSeq

Ruby

commute-times

4 1
calculate drive times from multiple locations and visualize them in google earth

davidapi

3 1
A ruby wrapper for a few of the DAVID API functions for functional gene annotation (http://david.abcc.ncifcrf.gov/)

iTunes-to-Guayadeque

2 0
copies song ratings from iTunes to Guaydeque music player

RMEmod

1 2
A tool for discovering functional modules by identifying recurrent and mutually exclusive mutational patterns in tumors

Shell

igvScreenshot

4 0
Create static screenshots of genomic regions using IGV.